Gundam Seed Destiny (Altered Timeline)
by DongLongQua
Summary: What if Shinn remained the protagonist until the end? The first chapter of this altered story is roughly the first 24 episodes of Gundam Seed Destiny. The second chapter is roughly episodes 25-37. The third chapter is roughly episodes 38-42. The Fourth Chapter is roughly episodes 42-50 (which is obviously very different from the original).
1. Chapter 1: A New Power

A/N: Hello. This is my first time posting here. I have written a lot of Fanfiction (mostly about Gundam) but I have never published it here before. I am a big fan of the Gundam Series and thus I am writing either altered versions of their story or originals based on existing material. There's just this thing about my writing: I always write in plot format. So please forgive me if you don't like this format or if the story becomes confusing.

A/N #2: Everything that happened in Gundam Seed (Remastered) stays exactly the same. The first part of this story doesn't have many changes from the original except for the major change that Meer Campbell doesn't exist in this story. Nothing personal, I just thought that the overall story would still work without her.

* * *

 **GSD I -A New Power**

* * *

C.E. 71 during the battle at Orb, Shinn's family was killed (due to the fight between the Freedom and Calamity). This causes Shinn to hate war and decides to become a soldier.

C.E. 73 two years after the war Gilbert Durandal and Caglli Yula Athha were in talks for a partnership between ZAFT and Orb, Cagalli refuses to provide military aid, but their meeting was cut short due to an incident in Armory One, three ZAFT Gundams were stolen. ZAFT sends in the Impulse, piloted by Shinn Asuka, to intercept the thieves. The Impulse is able to hold off the three but it was soon overpowered. Athrun saves Shinn by ramming his ZAKU on the Abyss. The Abyss retaliates by shooting its chest cannon, hitting the ZAKU on the arm. The impact wounded Cagalli's head and she fell on his lap, unconscious. Athrun is forced to retreat to the Minerva. Sting orders them to retreat because reinforcements were almost there. Stella blows a hole and they use it to escape outside.

Shinn and Rey follow them (Lunamaria's ZAKU was damaged and it went back to the Minerva. Athrun's ZAKU arrived shortly after her. She raised her guard at first but upon learning that the passenger was Cagalli Yula Athha, she immediately ordered the crew to take her to the medical bay. Neo bought time for the three to escape as he fought the ZAKU and the Impulse with his Exus to a stalemate. With the Impulse's power getting low, the Minerva launches, retrieves the two. The Minerva gives chase because it would be trouble if they left the Phantom Pain alone and they need to retrieve the stolen Gundams (destroy them if necessary). After a lengthy battle, the Phantom Pain was able to outmaneuver the Minerva and damage it enough to stop it at its tracks. The Minerva is forced to sit tight and wait for repairs.

While the Minerva was being repaired, Cagalli toured the ship with Gilbert. They unofficially "resume" their talk but is interrupted by Shinn who voiced out his personal hatred for the Athhas and Orb. This affects Cagalli in a personal way since she realized that many families like Shinn, and to some extent even her own, died for Orb and its ideals. Athrun comforts her in her room.

Meanwhile a terrorist group comprised of Patrick Zala loyalists, shifted Junius Seven's trajectory towards Earth. The Joule team was deployed to destroy it. The Minerva help the Joule team since they were near the site. Gilbert is able to convince Athrun to drop his Alex Dino persona and embrace his family name to fight for ZAFT once again. Athrun launches in a ZAKU to help out. He is reunited with Dearka and Yzak. They defeated the three Gundams and were able to destroy about 97% of it but the debris still hit Earth causing catastrophic levels of destruction. The Minerva goes to Orb for repairs.

While in Orb, Cagalli was surprised that the Parliament wanted to make an alliance with the EF. The crew of the Minerva disembark so that they can relax. Kira visits the Cenotaph. There he meets Shinn face to face. Athrun meets up with Kira and tells him about his experience in space. After their meeting, he decides to go to the PLANTs to try and convince Chairman Durandal not to escalate the tension between ZAFT and the EF. Before he goes, he gives Cagalli a ring; the two kiss, and Athrun goes to the PLANTs.

The EF retaliated after learning that coordinators were the one responsible for the drop. They fired nuclear missiles at the PLANTs but are stopped with the use of the nuclear stampeder. The citizens of the PLANTs go into a panic and shout war. But they are calmed down with the words of Chairman Durandal.

Back in Orb, Cagalli, not being able to do anything about Orb joining the EF, asks the Minerva to leave because she cannot protect it once the treaty has been signed. But as soon as they leave and an EF ambush was waiting for them. Orb meanwhile closes its doors to the Minerva. They are battered down pretty hard and when Shinn was about to be killed by a new mobile armor, he goes into SEED mode and destroys the mobile armor and many ships of the EF.

Athrun, in the PLANTs, hears about the Orb and EF alliance. Durandal talks him into rejoining ZAFT, and he does. Durandal personally promotes him to a FATIH member and gives him the Saviour. With a new Gundam, Athrun heads back to Earth. When he reaches the territory of Orb he tries to sneak in but was intercepted and was told to leave. He complies and heads for Carpentaria.

As Kira and the rest were cleaning up the debris form the fall, they learn about Cagalli and Jona getting married. This prompts them to launch and reactivate the Freedom and the Archangel. He "kidnaps" Cagalli and they escape unharmed. Kira and Cagalli argue about each other's actions. It ends with Cagalli accepting that what Kira (and the others) did was the right thing and she will do what she can to right the wrongs of Orb.

The EF forces lead by Neo and the Orb forces lead by Jona, attack and ambush the Minerva. The Freedom and Archangel arrives and assists the Minerva in escaping. They don't kill anyone. When the Minerva has escaped, Cagalli launched in the Strike Rouge and demanded that the Orb forces leave the area for this was not their [Orb] fight. Jona, not wanting to be humiliated in front of the Orb Admirals, responded by attacking her. This surprises everybody. Cagalli tries again but it was futile. Kira orders her to retreat since her presence is not helping, instead it might have made the situation worse. Shinn is unsure why he feels hatred towards the Freedom.

The Minerva arrives at Carpentaria. The crew meets Heine in the canteen and he tells them that he will be joining the Minerva. Afterwards the crew meets up with Durandal. They discuss various stuff. After the meeting, Shinn and Lunamaria went out for a totally platonic dinner together, while Athrun and Heine went out for some drinks. They talk about their pasts and about how they don't actually want to fight despite them being FAITH members.

Morning comes and the crew of the Phantom Pain goes in the city. Shinn, Lunamaria, and Meyrin decide to shop. Athrun stays in the ship and tunes up the Saviour (he also helped Heine transfer to the Minerva). Shinn meets Stella after he saved her when she fell from a cliff, injuring her ankle. They get stranded in a cave. Shinn used his handkerchief to bandage her injury. She gives him a beautiful pink seashell as a token of gratitude. Shinn promised her that he will protect her. They are later rescued by Athrun and Stella is reunited with Sting and Auel.

The Minerva heads out once again and heads for Gibraltar. They are instead met with yet another ambush by the EF forces. They fight desperately and fend them off. Shinn, after fighting the Gaia, notices a nearby POW work camp and liberates it. He is reprimanded by Athrun because of his actions.

They stop at a small ZAFT base near Morocco and resupply there. Since they were there, they were given a mission to liberate an EF occupied town and destroy the positron cannon defending it. They succeed and they receive medals for their work. Cagalli and Lacus talk, in the hot spring of the Archangel, about the right thing to do or what one believes as the right thing to do.

The Minerva heads back out and are ambushed (again) by a huge fleet of EF and Orb forces. The Freedom and Archangel arrive again but this time to fight all of those in the battlefield to try and make them stop. The Minerva is very heavily damaged. In the melee, Kira accidentally kicks Heine's GOUF into a charging Gaia, killing him instantly. The EF and Orb forces retreat when they were torn apart by the Sword Impulse and an angry SEED-mode Shinn.

The Minerva docks somewhere near Crete to repair and resupply. While they are there, Shinn and Rey are given a mission to scout a suspicious facility in a nearby city. Athrun asks Captain Gladys if he can leave to meet with Kira. She agrees but secretly sends Lunamaria to spy on him.

With the help of Miriallia, Athrun was able to meet with Kira and Cagalli. They argue about their actions. Athrun is angry that Cagalli just went out and tried to stop the Orb forces and that she put herself in danger. Cagalli defends her actions saying that Orb shouldn't be fighting and she is doing everything she can to stop Orb from destroying itself once again. Kira takes Cagalli's side and defends her actions. Cagalli pleads to Athrun to help her stop Orb peacefully. Athrun tells her that fighting is now inevitable and peaceful solutions are futile. Athrun is then called back to the Minerva but before he leaves, her notices that Cagalli was still wearing the ring. Athrun asks her if she hates him now or if she will if he continues to fight against Orb. Cagalli answers him with one word: Never. He regains his composure and tells the others to just lay low and stop creating confusion on the battlefield. Cagalli tearfully watches him go.


	2. Chapter 2: The Certain Uncertainties

**Pinned A/N** : Hello. This is my first time posting here. I have written a lot of Fanfiction (mostly about Gundam) but I have never published it here before. I am a big fan of the Gundam Series and thus I am writing either altered versions of their story or originals based on existing material. There's just this thing about my writing: I always write in plot format. So please forgive me if you don't like this format or if the story becomes confusing.

 **Pinned A/N #2** : Everything that happened in Gundam Seed (Remastered) stays exactly the same. Meer Campbell doesn't exist in this story. Nothing personal, I just thought that the overall story would still work without her.

A/N: This chapter may not look like it has any major changes but most of the changes have to do with character's motivations and reasons. Also I think that the ZGMF-X23S Saviour had a lot of missed potential so I retconned its destruction and brought it back as the Saviour Repair (just think of the Exia R1 and apply it to the Saviour). Also I didn't want Athrun just sitting around doing nothing when the Saviour was destroyed.

* * *

 **GSD II – The Certain Uncertainties**

* * *

Shinn and Rey discover an abandoned Extended facility of the EF. Rey reacts negatively and is brought back to the Minerva. Talia and Arthur make a thorough investigation and discover a lot of info about the Extended program.

The Phantom Pain hears about the infiltration, and Auel goes paranoid thinking his mom would die if ZAFT keeps poking around. Sting tries calm him down but Stella heads off to the facility in the Gaia after hearing her block word.

The Saviour and Force Impulse intercept and disable the Gaia. Shinn discovered that Stella is the pilot; he immediately brings her to the medical bay of the Minerva. This obviously confuses everyone. Rey reported the incident to the higher ups, Soon enough, Captain Gladys receives word from the council that they want a living extended brought to them for examination ASAP. So they decide to head out after resupply and repair.

They head out and the largest EF and Orb force ambush them. They fight desperately but the Freedom and Archangel appear once again and attacks everyone on the battlefield. Cagalli also heads out and tries to stop the Orb forces in the area to stop attacking the Minerva and go back to the mainland.

Her words do nothing but anger Shinn, causing him to fire eight missiles at her. The Freedom uses its Picus to shoot down all missiles. It charges at the Blast Impulse but the Saviour intercepts it before the Freedom can get close.

The EF and Orb force resume their attack on the Minerva and the Archangel. Captain Gladys declares the Archangel their enemy. The Murasames charge at the Minerva but Cagalli uses the Strike Rouge to block their path. She learns that the Sarans now rule Orb (and in turn, are puppets of the EF). Baba's Murasame throws the Strike Rouge out of the way and resumes their charge on the Minerva.

Lunamaria and Rey desperately tried to defend their ship but they couldn't stop the barrage of missiles and machinegun fire. Lunamaria's Gunner ZAKU was totaled, injuring her.

Shinn destroys the Abyss and kills Auel. Athrun once again tries to talk Kira into stopping. Kira ignores him, disables the Chaos, and engages the Blast Impulse. Shinn suddenly remembers the Freedom from two years ago and attacks it angrily. Even though he was a match for the Freedom, he was ordered by Athrun to return and help the Minerva because Lunamaria got injured and her ZAKU is out of action.

Shinn switches to the Force silhouette. Baba and his squad go for one last kamikaze charge on the Minerva. The Force Impulse was able to shoot down all Murasames except for Baba's, who successfully rams his Murasame on the Minerva, inflicting heavy damage on its bow (and also damaging Rey's Blaze ZAKU Phantom).

Shinn switches to the Sword silhouette and destroys numerous mobile suits, warships, and carriers from both EF and Orb. Cagalli tries to stop him but is no match for Shinn. A squad of loyal Orb soldiers forced Cagalli to retreat.

The Takemekazuchi charges the Minerva. The Minerva was still able to inflict crippling damage to the carrier. The crew (and Jona) of the Takemekazuchi abandon ship and [those who are still loyal to Cagalli] head to the Archangel as per Colonel Todaka's orders.

Kira and Athrun battle it out because he thinks that Kira is endangering Cagalli by putting her in the front lines (among other things) but Kira tells him that Cagalli is really trying her damn best to stop Orb from participating in the war. The two argue and fight a little bit more but the Freedom ultimately defeats the Saviour. Shinn destroys the Takemekazuchi, killing Colonel Todaka.

Lacus tells Kira that she wants to go to the PLANTs to gather more information about Durandal. Kira objects but Lacus convinces him to let her go. Lacus and Waltfeld disguise themselves and snuck past ZAFT soldiers and checkpoints in an airport. They are found out and the Captain of the military police order his men to shoot down the shuttle Lacus was on.

Several mobile suits shoot the shuttle but before they can hit it, the Freedom enters the scene and disables all the mobile suits in the area. Kira contemplates on whether he needs to go with Lacus. She tells him to stay with the Archangel. Waltfeld promises Kira that he will protect Lacus with his life. Kira asserts that Lacus needs to be careful but before they could say anything else, the communication was cut. Lacus successfully escapes.

Durandal hears about Lacus' stunt and he realizes that she's up to something. He tasks Special Forces to follow her and if need be, eliminate her.

The Minerva goes back to the base at Crete for repairs. Stella's condition worsens and is at the brink of death. This caused Shinn to sneak her out [return her to Neo]. But before he can, Rey catches him. They talk a little and Rey decides to help Shinn. Rey hacks the gates and let's Shinn out in the Impulse. He contacts Neo; they meet and he gives Stella back. With the promise of keeping her away from war and fighting, they part ways.

Shinn returns and is thrown into a holding cell. Rey is also thrown in a cell for his participation. Athrun hears about what Shinn did, but decided not to say anything to the authorities. He talks to Shinn privately and tells him that he will side with him if worse comes to worse.

In Germany the EF deploys their new weapon, the Destroy. The pilot chosen for it was Stella. The Destroy, Chaos, and Neo's Windam wreak havoc in Germany. Shinn is cleared and released because of his achievements recently (and because he was the only ace pilot with a properly working Gundam). After hearing about the events in Germany the Minerva [is ordered to] and the Archangel [decides to] go there.

The Archangel arrives first and the Freedom engages the Destroy (they intercept it in Berlin). Cagalli, in the Strike Rouge, engages the Chaos and the Murusames engage the Windam. The Freedom can't seem to harm the Destroy. When the Minerva arrives, Shinn and Kira team up for a while. The Impulse destroys a portion of the cockpit hatch and sees that the pilot is Stella. He calmly approaches and the Destroy stops attacking. The Saviour Repair launches. Athrun teams up with Cagalli and together they defeat the Chaos. The Freedom shoots down the Windam. Kira tells Murrue to retrieve the fallen pilot.

This causes Stella to panic and start attacking again. Kira then tries to attack the Destroy but instead, Shinn attacked him. Cagalli and Athrun tried to damage or at least distract the Destroy. The Strike Rouge and the Saviour Repair then come up from behind and destroy its main battery pack, causing the Destroy to slowly lose power. The Impulse and Freedom battle it out, and as the Freedom was about to stab the Impulse dangerously close to the cockpit, Stella uses the last bit of the Destroy's backup power to shove the Impulse away and use the huge mobile suit as a shield. The Freedom instead stabs the chest cannons of the Destroy. Stella saves Shinn but she gets caught in a fatal explosion. The Archangel and crew then retreat as ZAFT reinforcements arrive.

Shinn holds a dying Stella in his arms and she kisses him after declaring her love for him and dies shortly after. This causes Shinn to hold a grudge against the Freedom (and its pilot).

Chairman Durandal uses the Berlin incident as a reason to declare the LOGOS as the true enemy of mankind. The Archangel is also labeled as a target and the ZAFT Eurasian force was sent to sink it. Minerva is also ordered to participate in the Operation (Operation Falling Angel). Shinn, in a rage fueled motivation, has studied and analyzed the Freedom's fighting pattern. Athrun refuses to participate in the mission.

Shinn uses the Impulse's block system to gain a significant advantage over the Freedom. Not only does he isolate the Freedom, he also prevents it from helping the Archangel. The ZAFT Eurasian force use overwhelming numbers to slowly but surely surround and pressure the Archangel. The Force Impulse is able to significantly damage the Freedom, forcing Kira to retreat.

As the Archangel approaches the sea, the Minerva fires its positron cannon at the Archangel in hopes of sinking it before it can dive. The Force Impulse impales a retreating Freedom below the cockpit (closer to its waist) allowing Kira to survive. There was no nuclear explosion. The Freedom exploded normally because Kira cut off the power of the Freedom at the last second. Shinn wonders of he did the right thing, and if what he did really avenged Stella.

Back in the Minerva, Shinn goes straight to his room and contemplates. An angry Athrun follows him and talks with him privately. Shinn reveals that he knew he missed the Freedom's cockpit and that the pilot may have survived. He explains that he got brief glimpse of Stella before he impaled the Freedom. Athrun is pleased to hear this but his doubts about ZAFT increases. He tries to emotionally support Shinn in his troubled state.

Kira awakens and talks to Neo (thinking that he is Mu la Flaga) but Neo assures him that he is not the man Kira thinks he is. Murrue suddenly enters and asks Kira if he is alright completely ignoring Neo. But Neo asks about Mu, making Murrue run away, crying.

The Minerva arrives at Gibraltar and Chairman Durandal requests to meet with Shinn and Athrun. He shows them latest machines from ZAFT; the ZGMF-X42S Destiny and the ZGMF-X666S Legend. Athrun is displeased with the offer while Shinn accepts the Destiny. After showing the Destiny and Legend to them, Athrun decides to go back to his room and think.

Chairman Durandal meets with Rey and asks him about what he thinks of Athrun. He tells him that he [Athrun] is a threat to the plan and must be eliminated. Durandal agrees, and plans to charge him with a crime (treason; thanks to Lunamaria's spying) and have Rey take care of the rest. Shinn overhears this and immediately goes to Athrun's room to tell him about it.

Athrun realizes that Durandal has no more need of him and decides to run away. He tries to take Shinn with him but he refused. Saying that there may still be a chance to change his [Durandal] mind. Athrun sternly tells him that that is not possible; that the Chairman is very manipulative and one day, will have no more need of him [Shinn], and eventually kill him. He also asks how he plans to run away and he said he'll think of something.

After a few minutes, the guards knocked on the door demanding Athrun. Athrun then punches Shinn, breaks the window, and apparently escapes. The guards enter and find Shinn on the ground saying that he tried to stop him but got knocked to the ground. As one of the guards look out the window, Athrun knocks him, and the other guards out. Shinn then tells him to stick to the plan and they go their separate ways.

Athrun then ends up in Meyrin's room. Lunamaria and other guards knock at her door, she [Meyrin] covers for him by answering the door, pretending that she just came from the shower. Lunamaria gives her some time to dress up and she closes the door. Athrun asks why she helped him she responds with "I don't know". As he was about to leave, Meyrin stops him and decides to help him more. She hacks the computer and sets off an alarm by the Bay (the other side of the base) luring the pursuers there.

They escape using her car, but Rey sees Meyrin and gets suspicious. They arrive at the hangar and decide to board the Saviour Repair. Rey then pops out, starts shooting and declares them both traitors. Athrun tries to convince Rey to let Meyrin go but to no avail. Athrun shoots Rey's gun, causing him to drop it, and the two used the opportunity to board the Saviour Repair.

Rey contacts Shinn about Athrun escaping. Durandal orders them to pursue. Rey informs Durandal about Meyrin's choice to go with Athrun and they get the all clear to shoot them down. Shinn is surprised that Meyrin is with Athrun. They confront each other and Shinn "tries to talk him into surrendering" but Athrun flat-out refuses. Rey tells Shinn to kill them because even Meyrin has become an accomplice to Athrun's crimes. Shinn begins to realize the truth to Athrun's words. The Destiny impales the Saviour Repair; purposely missing the cockpit. It [Saviour Repair] falls to the sea and explodes. Rey didn't notice Shinn missing the cockpit and just presumed that they both died. The two return to base.

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A/N #2: Honestly, can this plot be turned into a 2 hour movie? Just a random thought. Also, I know there are a lot of brackets here; I just want it to be less confusing as possible.

A/N #3: I promise there will be major changes in the next chapter.


	3. Chapter 3: A War For One's Self

**Pinned A/N: Hello. This is my first time posting here. I have written a lot of Fanfiction (mostly about Gundam) but I have never published it here before. I am a big fan of the Gundam Series and thus I am writing either altered versions of their story or originals based on existing material. There's just this thing about my writing: I always write in plot format. So please forgive me if you don't like this format or if the story becomes confusing.**

 **Pinned A/N #2: Everything that happened in Gundam Seed (Remastered) stays exactly the same. Meer Campbell doesn't exist in this story. Nothing personal, I just thought that the overall story would still work without her.**

A/N: OK, major changes are here. I'm sorry if characters here act weird but I tired to make it as detailed as possible while making as short as possible. I also did not include the three DOMs and its pilots because I didn't think they were a necessary part of the story.

* * *

 **GSD III – A War for One's Self**

* * *

Everyone [in the base] is shocked to hear the incident. Durandal personally confronts Lunamaria about Meyrin's betrayal; Lunamaria is shocked beyond belief. Rey and Shinn were walking in the hallway when they bump into Lunamaria. Shinn pulls her to his room so that they can talk alone. Rey assumes nothing bad and leaves them be. Shinn tells Lunamaira the plan they [Shinn and Athrun] came up with.

Athrun was to punch Shinn (to make it look like a struggle) and escape in the hangar to get to the Saviour Repair. Durandal is going to order Shinn to shoot him [Athrun] down to test his [Shinn] loyalty; he will, but he must stab it away from the cockpit so he [Athrun] can escape. Athrun plans to go to the Archangel in ORB.

But the plan didn't account for Meyrin, and therefore he was shocked. He [Shinn] still followed the plan and did not stab the Saviour Repair in the cockpit. They may have been hurt but they are definitely not dead. This makes Lunamaria happy but Shinn tells her that no one must know, especially Rey and Durandal. She agrees to the secret, and asks him what he plans to do next. Shinn replies with "I'm not sure." Durandal initiates Operation Ragnarok (assault on Heavens Base). Kisaka secretly retrieves the cockpit of the Saviour.

A few hours before they head for Heaven's Base, Lunamaria enters Shinn's room and thanks him for not killing Meyrin. After talking about how their relationship will go from now on, they proclaim their love for each other and make love for the first time. ZAFT gives EF an ultimatum of five hours to turn over the head Logos members, to disarm, and surrender. They don't respond and instead, attack first.

Athrun wakes up in the Archangel and talks to Kira.

Five Destroy units crush the EF defectors and the ZAFT combined force. ZAFT tried to send reinforcements via air drop but Djibril uses the Nibelung to destroy all of the Mobile Suits in the air. Durandal orders the Minerva pilots to sortie.

They all sortie and easily destroy the Destroy units (and other mobile suits). The three Gundams rip through the rest of Heavens Base defenses with ease. The Destiny impales the last Destroy unit with its Arondight, killing its pilot, Sting Oakley. Djibril prepares to escape in a stealth submarine.

Athrun tells Kira about what happened to him. Kira assures him that Shinn will eventually join them. Athrun agrees. Cagalli enters the room and tearfully hugs Athrun. Heavens Base falls but Djibril escapes and heads to Orb.

Martin DaCosta searches the remains of the Mendel Colony and finds a notebook. As he heads back to the Eternal, a reconnaissance GINN follows him.

After the fall of Heavens Base, Shinn and the rest heard that Djibril has escaped. Shinn wonders what Durandal's next move will be. Rey talks to him about his [Shinn] relationship with Lunamaria; saying that it might not be the best course of action for him. Shinn defends his relationship with Lunamaria; Rey starts to get suspicious.

In the Archangel Athrun and Cagalli talk about their decisions and actions towards each other. They eventually forgive each other for acting the way they did. Athrun asked Cagalli if he can start again (and this time he will do it right) to which she replies a very wholehearted "Yes".

Back in space, Lacus and Andrew Waltfeld discuss the contents of the notebook which contains a very rough draft of the Destiny Plan from when before Durandal was Chairman. But before long the reconnaissance GINN shoots the perimeter security camera of the Eternal. Knowing that they've been found out, they ditch their camouflage and launch at full speed. The three Nazca class ships that have been following them, pursue them. Lacus orders the crew to head near Earth so that they can drop the Gundams on Earth if worst comes to worst.

Kira hears about the Eternal's situation and borrows Cagalli's Strike Rouge Ootori (and a space booster). The Eternal is being shot from all directions. While clever maneuvering and aiming has prevented them from being sunk, the continuous pressure from the enemy forced Commander Waltfeld to sortie in the Gaia. He, too, is overwhelmed but at the last second, the Strike Rouge Ootori arrives just in time to save the Gaia and the Eternal. It takes out a couple of suits before Waltfeld ordered Kira to inside the Eternal and get his new Gundam.

He goes in; Lacus hugs and greets him. She takes him to the hangar and shows him the Strike Freedom. Lacus tells him that its Hyper-Deuterion Engine was not yet ready, so it will be running on an emergency battery that can operate for a maximum of 5 minutes.

The Strike Freedom launches and defeats a total of 25 mobile suits (ZAKUs and Goufs), and three Nazca-class ships in a little over two minutes. The Strike Freedom runs out of power as it returns to the Eternal.

Shinn, Rey, and Lunamaria receive medals for their work on Heavens Base. Furthermore, Shinn and Rey are promoted to FAITH. Shinn hacks the camera of the room where Durandal was having a meeting. He hears that Djibril is in Orb and that the Chairman will use that as an excuse to finally burn Orb to the ground (with the help of the Destiny and the Legend). Shinn realizes that what Athrun said is true (The Chairman uses everyone like pawns and that he [Shinn] was the best pawn the Chairman could ever have).

He decides to defect, but before escaping, he goes to Luna's room and tries to convince her to come with him. She declines and argues that he will be declared a traitor and be killed. Shinn tells her what he heard. The two start to argue, but suddenly Rey, who has been listening to Shinn, bursts in the room with a gun and tries to arrest Shinn for treason (he also threatens Lunamaria if she will defect with Shinn).

Lunamaria emotionally froze and falls to the floor crying. Shinn tries to convince her one more time but Rey interrupted, and shot Shinn in the chest. He falls to the floor. Lunamaria rushes over to him but Rey shoves her away. Suddenly, Shinn kicks the gun out of Rey's hand, and knocks him down. Shinn grabs Rey's gun, smashes the window, and escapes. Rey calls for back up, follows Shinn to the hangar, and alerts Durandal. After a short gunfight, Shinn was able to get to the Destiny, although he was shot in the left leg and the right shoulder, he activates it, and flies out to the sea. The Legend chases and open fires on him. He evades, and cleverly uses his surroundings and the Destiny's Wings of Light to quickly escape. Shinn pulls out a thumb drive and his medal from his breast pocket. It turns out the medal deflected the bullet, saving his life.

Rey stops his pursuit knowing full well that the Legend won't be able to catch up with the Destiny. Rey reports the incident and tells Durandal that Shinn has nowhere to go. Durandal suspects that he might go to Orb. He tells Rey that they need to take out Orb now so that Shinn will not have time to leak any information. After carefully flying under the radar for a few hours, Shinn finds the Archangel's dock (using the thumb drive given to him by Athrun before he escaped).

Everyone is surprised to see the Destiny approaching, and they scramble a few Murasames on him, but Shinn puts away its weapons and surrenders. Meyrin asks Cagalli to tell the Murasame pilots to escort the Destiny inside the Archangel. The Destiny lands inside and the moment Shinn hits the ground, he collapsed from blood loss. Meyrin and Athrun help bring him to the medical bay.

Athrun visits Shinn as soon as he woke up and asks him what happened. Athrun promises Shinn that they will make things right. ZAFT's ultimatum (of surrendering Djibril) was up and they have begun their assault on Orb.

An all-out war begins between ZAFT and Orb. Cagalli asks for Shinn help. He tells her that the he won't let the past control his feelings anymore and agrees to help. She thanks him and rushes back to the bridge of the Archangel and demands that she join the battle as well. Murrue disagrees since there is no spare mobile suit for her to use. Cagalli demands to use the Sky Grasper, Kisaka and Erica Simmons (who overheard the entire conversation) take her to a nearby offsite hangar of Morgenrate; in the chamber of the Akatsuki.

Cagalli listens to her father's last will; having a reformed will, she decides to pilot the Akatsuki to protect Orb. Athrun walks with Shinn to the Destiny. He asks him to protect Cagalli out there. He promises to do so. Before Shinn closed the hatch, he apologizes to Athrun about everything. He [Athrun] says that they will have plenty of time to talk once he gets back. Murrue frees Neo (since they are about to go to war and she doesn't want him to get involved) and gives him the Sky Grasper. She cries as she runs back to the Archangel, leaving Neo confused.

Shinn stands by. Cagalli tricks Jona Roma Seran into acknowledging her as Orb's military commander; she orders his arrest for treason. She then assumes command of the Orb defense force and they start to push back the ZAFT forces. Their advance is short lived when the Minerva arrives and Rey launches in the Legend. It engages the Akatsuki. The two trade shots and clash beam sabers. Athrun sits in the CiC of the Archangel; so does Meyrin. The Destiny launches.

The Akatsuki is easily overpowered by the Legend; with the Akatsuki losing an arm and its shield, Rey goes for the killing blow but suddenly the Destiny shot the Akatsuki and ricocheted the shot from its High-Energy Long-Range Beam Cannon towards the Legend, stopping its charge. The Archangel launched, and engaged the Minerva. With ZAFT gaining the upper hand once again, the Akatsuki retreats and assists the Orb defense force.

Shinn and Rey fight, but due to his injury, he cannot fight at full potential. The Strike Rouge Ootori, piloted by Kira, and the Infinite Justice, piloted by Lacus (also a descent pod) suddenly descend from the sky. The Strike Rouge Ootori distracts the Legend so that Shinn can get his bearings (he injects a shot of painkiller). Kira tells Lacus to go to the Archangel so that Athrun can use the Infinite Justice (and also take the pod there).

Cagalli leaves the Akatsuki just outside the Defense Ministry building. She meets with the commanders, and orders them to find Djibril, slugs Jona, and tells the guards to take him away. Shinn tells Kira to leave Rey to him. He agrees and goes off to defend Orb. Lacus meets Athrun inside the MS hangar of the Archanghel. They talk about whether he should return to the battlefield or not. But Athrun ultimately decides to return and pilots the Infinite Justice. The Infinite Justice launches to help the Destiny.

The Minerva and the Archangel are busy fighting each other, when suddenly the Sky Grasper swooped in to help the Archangel. The Sky Grasper was damaged and boarded the Archangel for repairs. As the Destiny, Infinite Justice, and Legend battle it out, the high ranking Orb ministers, and Jona are killed by a ZAFT infiltration team, and a falling GOUF respectively.

The Strike Rouge Ootori suffered heavy damage by the sheer number of enemies Kira took on (alone). Cagalli tells Kira to use the Akatsuki instead. Djibril uses the chaos in the battlefield to escape, and takes a shuttle headed for space. The Minerva (and Orb) detect the shuttle launching; they send Lunamaria in the Force Impulse to shoot it down; she misses. Kira also chases it, but the Akatsuki ran out of fuel before getting within firing range of the shuttle. Djibril escapes to space.

The Archangel dives underwater to evade the Minerva. When Shinn and Athrun entered SEED mode, the Destiny and the Infinite Justice were able to inflict heavy damage to the Legend. Rey's left eye was blinded when the cockpit computers exploded.

The Archangel sank the St. Helens; the Minerva assumes command and calls for all ZAFT forces to retreat. The Destiny points its gun at the retreating Legend but Shinn hesitates and doesn't fire. Athrun tells him that he's done enough; the two head back to the Archangel.

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A/N #2: I really just wanted to make an Evangelion reference via the Strike Freedom (5 minute operation time on battery). I also made Kira use the Strike Rouge Ootori during the defense of Orb to show that Kira doesn't solely rely on beam spam to kick ass.

A/N #3: Next part will be the last part. (seriously if this were to be a movie, is 2 hours enough to cover all this?)


	4. Chapter 4: The Light That Guides The Way

**Pinned A/N: Hello. This is my first time posting here. I have written a lot of Fanfiction (mostly about Gundam) but I have never published it here before. I am a big fan of the Gundam Series and thus I am writing either altered versions of their story or originals based on existing material. There's just this thing about my writing: I always write in plot format. So please forgive me if you don't like this format or if the story becomes confusing.**

 **Pinned A/N #2: Everything that happened in Gundam Seed (Remastered) stays exactly the same. Meer Campbell doesn't exist in this story. Nothing personal, I just thought that the overall story would still work without her.**

A/N: Some important info you need to know before reading the final part:

The **ZGMF-X676T** **Legend Performante** is a slightly bulkier version of the Legend, with **four beam rifles** (two in hand and two on the back), **30 DRAGOONS** (6 regular and 2 large on the backpack, 4 regular on each side skirt, 4 regular on the back skirt, 1 regular for each front skirt, and 4 regular on each shoulder), and **the HFES** [High Frequency Environment Scanning] **system** ; two half rings each connected to a sub arm comes out of the backpack that either lifts connects [to form a circle] above the Legend's head as a super antenna of sorts or in front of the Legend as a positron reflector.

The **METEOR Mk II** ; just imagine if the Narrative A-Packs and the METEOR had a baby

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 **GSD IV – The Light That Guides The Way**

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Durandal tells Gladys that she made the right call ending the battle after Djibril escaped. Gladys reports Shinn's involvement in their [ZAFT] defeat, and her concerns about Lunamaria's loyalty.

In the Archangel, Athrun gets out of the Justice but quickly falls to the floor. Shinn opens up his suit and sees blood, Kira quickly called for a stretcher and a medic. Shinn's leg also starts bleeding again. Kira helps him to the medical bay. (A few hourse later) Athrun, trying to get up again is helped by Meyrin to sit up. Kira and Lacus visit and told him that they're happy that they can talk again as friends. Cagalli heads to the Orb Palace to make an international broadcast.

Murrue and Neo talk on the deck (of the Archangel) and he tells her that he definitely knows her and asks if he can stay by her side. She nods and the two hug. (In the viewing deck of the Archangel) Kira thanks Shinn for protecting Cagalli and Orb. He also apologized for what happened in Berlin. Shinn tells him that they were all just did what they thought was right and forgives Kira. Meyrin also showed up to talk to Shinn. Shinn apologizes for putting her life in danger. She tells him that there is nothing to apologize for. Meyrin worries for the safety of Lunamaria. Shinn assures him that she will be safe, and that he will get her back. He accidentally reveals that he and Lunamaria are together. She is happy for them and wishes them luck on their relationship.

Cagalli's broadcast begins. She calls out the doings of Durandal and why he had to attack Orb, her broadcast was suddenly cut short when Durandal interrupts with his own argument. Lacus decides to appear with Cagalli and interrupts Durandal's to make a speech of her own. The people are now confused as to who to believe.

Lunamaria visits Rey in the medical bay to ask about the (Durandal vs Lacus) situation. He tells her that it doesn't matter; as long as they are with ZAFT, they should follow the Chairman's orders. Rey also question her loyalty but she assures him that her loyalty is with ZAFT. Rey (revealed to be wearing an eye bandage) remains suspicious. Lunamaria (obviously deeply affected by the situation she was in) cries in the shower.

With Djibril at the Daedalus Lunar Base, he orders the EF commanders to position old abandoned colonies (Relay Stations) equipped with massive Geschmeidig Panzers into firing position, A ZAFT task force led by Yzak Joule, discovers the relay station Gounod. A battle between ZAFT and EF ensues. The Requiem fires. Battle damage to Gounod slightly altered the trajectory of the beam, and as a result, Requiem missed its intended target. Instead, the beam directly hit and destroyed Januarius 1 through 4 which hit December 7 and 8 causing it to collapse, leading to the deaths of over a million Coordinators. Afterward, the Joule Squadron destroyed the Gounod relay station, but Djibril didn't pay much care since the Requiem's design is such that other stations can still be used to aim its beam at PLANT. Furious, Durandal orders the Minerva to head to space.

Kira, Athrun, Lacus, Cagalli, Shinn, and the rest discuss the Destiny Plan, the Requiem, and Logos. They all decide that each one of it must be stopped and make preparations to head up into space. Rey looks at his repaired and upgraded Legend, the ZGMF-X676T Legend Performante.

Durandal orders the a massive ZAFT Force to attack one of the relay stations, while the Minerva snuck to the Daedalus Lunar Base to destroy the cannon itself. A few minutes before they sortie, Rey warns Lunamaria that the assault on Daedalus will be a loyalty test for her. The Legend Performante (using the full potential of the HFES system) and the Minerva distract and destroy the Daedalus defense force. Lunamaria, in the Blast Impulse, snuck in the base itself and destroyed the control room, seconds before the Requiem was fired again. A well placed Tannhäuser shot destroyed the command center. Djibril tries to escape (in the Phantom Pain) again as the base falls but Rey spots him and kills him.

Erica Simmons (and her crew) completes the Hyper-Deuterion Drive of the Strike Freedom. Cagalli gives a speech that officially acknowledges the crew of the Archangel and the Archangel as a part of the second space fleet of Orb. She also tells everyone that she will be going with the Archangel for its mission (intelligence gathering).

Athrun expresses his concerns with Cagalli going with them. They argue for a bit but Athrun eventually agrees and promises to protect her. Cagalli takes off her ring and gives it back to Athrun. She tells him that the next time he puts it on her finger is when he bends the knee. He agrees, and the two kiss. Shinn and Kira teasingly calls for the two to get ready.

High-ranking officers of ZAFT report to Djibril that they have captured the Requiem and are currently repairing it.

The Archangel is in space. They head to Copernicus City. Lacus felt cooped up (having been inside a ship for months) so she decided that she wanted to visit the mall and go shopping (this was also a recon mission). Athrun was the first to object but Kira assured him that they can protect her. Meyrin also tags along. Shinn and Cagalli chose to stay with the Archangel because they needed to tune the Destiny and the Akatsuki. Mu asks Murrue if she wasn't going out, she tells him that she's used to being in a ship. Mu tries (and fails) to flirt with Murrue.

Lunamaria is still cooped up in her room, thinking about Shinn; Rey gets an artificial eye implant (a miniature auxiliary sensor which glows red when turned on).

While they were out shopping Kira angers Lacus because she thinks he doesn't care what she wears (or look like). Lacus then decided to visit a theater where she once performed but as they looked around, they were ambushed. Kira calls for backup and they eliminate all the assassins. The Destiny arrives and gives them a ride back to the ship.

When they got back, Durandal announces the defeat of Logos and the implementation of the Destiny Plan. Cagalli makes a live broadcast against the Destiny Plan. The young King George of Scandinavia also oppose the said plan. The president of the Atlantic Federation opposed it too but wanted to talk to Durandal about it. Their EF fleet stationed in Arzachel has begun to mobilize. As a result, Durandal used the Requiem they repaired to destroy the EF fleet at Arzachel, and killed the EF President. Orb, Kingdom of Scandinavia, and Terminal forces decide to destroy the Requiem and stop Durandal once and for all. Durandal orders the Minerva to go to Station One and join the ZAFT Lunar fleet in its defense. He orders Rey and the Legend Performante to go to the Messiah.

The Second Space fleet of Orb commence their assault on Station One. The Strike Freedom and the Infinite Justice launch equipped with METEOR. The Destiny launches with a booster pack. The Akatsuki, piloted by Cagalli, protects the Eternal, while the Gaia, piloted by Mu, protects the Archangel from ZAFT forces.

The Lunamaria, in the Force Impulse, launches and spots the Eternal. Meyrin communicates with Lunamaria, as she was about to fire on the Eternal, and persuades Lunamaria to stop her attack on the ship. Cagalli spots the Force Impulse and thought that it was attacking the Eternal. They exchange a brief clash of beam sabers until Shinn arrived and told Cagalli to help the Strike Freedom and the Infinite Justice.

The Minerva fired its positron cannon at the Archangel (if the Archangel evades, the shot will hit the Eternal). The Akatsuki and the Gaia block the shot. This causes Mu to regain his memories. The Gaia shoots the Tannhäuser, destroying it.

Shinn and Lunamaria argue whether they are doing the right thing. After a brief argument, Shinn gets out of his cockpit and reaffirms his love for Lunamaria. The Strike Freedom and the Infinite Justice provided cover for the two. Lunamaria chooses love over duty; she gets out of the cockpit of the Force Impulse and hugs Shinn. Athrun reminds them of the situation they are in. They get back in their Gundams and head for Station One.

The Destiny, Strike Freedom, and Infinite Justice soon destroy Station One but their victory is short lived when they realize that another station is coming to replace Station One. The space fortress Messiah advances to the front lines and fired the Neo Genesis at the Orb space fleet, wiping out nearly half of their forces. Rey takes drugs to enhance his senses, reaction, and instinct to the max. The Infinite Justice removes its METEOR to give the Eternal more offensive capabilities.

The Legend launches, equipped with the METEOR Mk II, and goes directly for the three Gundams (Strike Freedom, Infinite Justice, and Destiny). They gang up on him but they soon realize that he is just stalling, Kira decides to go and destroy the Neo Genesis (and the Messiah itself if possible). Shinn tells Athrun to destroy the Requiem and that he will deal with Rey. Athrun tries to argue but Shinn tells him that he will not hesitate anymore. Athrun and Cagalli go for the Requiem. The Destiny and the Legend battle all out. The Minerva reengages the Archangel. The Force Impulse is joined by the Joule Team in defending the Eternal.

Rey decides to try and hurt Shinn by telling him that he will kill Lunamaria first. The Legend Performante heads for the Eternal but just before it can fire upon it, the Destiny was able to destroy the METEOR Mk II. The Destiny is able to lure the Legend Performante away from the Eternal.

Kira is struggling with the amount of forces that are guarding Messiah (and its powerful shields); the Kusanagi is having a hard time in penetrating the Requiem's shields. Due to the fight between the Minerva and the Archangel, the Gaia sustained heavy damage but continues to defend [the Archangel]. The Infinite Justice destroys the engines of the Minerva causing it to lose power and crash on the Moon. Captain Gladys orders her crew to abandon ship.

Durandal orders the Neo Genesis to fire to eliminate the Orb forces near the mouth of the Requiem. The Strike Freedom ditches its METEOR and was able to slip in the moment the Messiah lowers it shields to fire the Neo Genesis. The shot destroys more of the Orb space fleet but also destroys some of the ZAFT forces.

With only 30 seconds before it [Requiem] fires, the Infinite Justice and the Akatsuki penetrate the Requiem's shields, and sacrifices its Fatum-01 and its DRAGOONS, respectively, to destroy the Requiem.

Despite the Destiny destroying multiple DRAGOONS, the Legend Performante was still able to gain the upper hand when it destroyed the Destiny's Anti-Ship sword, beam rifle, left arm, and right leg. The Legend Performante kicks the Destiny onto the moon's surface; Shinn loses consciousness from the crash.

The Strike Freedom destroys the Neo Genesis and the Messiah's shield generators. The Messiah slowly starts to fall on the surface of the moon. Lunamaria, seeing that the Destiny was in trouble, goes to fight the Legend Performante. The Force Impulse was no match for the Legend Performante and sustained mild damage. Lunamaria shouts at Shinn to wake up.

While unconscious, Shinn has a vision of Stella; she tells him that even though she doesn't have a future anymore, she was still happy for their brief but meaningful moments together and that Shinn still has a future (with Lunamaria).

Shinn awakens in SEED mode as the Legend Performante (using a beam saber) was about to deliver the final blow to the Destiny. The Force Impulse blocks the way with its shield. The Legend Performante tries to stab the Force Impulse instead. The Destiny suddenly activates the full power of the Wings of Light. It envelopes the Force Impulse, protecting it from the beam saber. Shinn orders Luna to separate the chest flyer; Shinn charges in with the Destiny's Palma Fiocina. It dissipates the beam of the Legend Performante's beam saber; the chest flyer of the Force Impulse shoots the Legend Performante, destroying both its arms and head, allowing the Destiny to obliterate the entire left side torso of the Legend Performante, permanently disabling it.

The Akatsuki recharges its batteries and equips the Oowashi Sky Pack. The Infinite Justice and the Akatsuki go to where the Messiah is. Yzak's ship fires a Deuterion beam to recharge the Force Impulse's battery.

The Destiny and the Force Impulse regrouped with the Strike Freedom, Infinite Justice, and Akatsuki to help destroy the Messiah's defenses. The Legend Performante limps back to the Messiah. Capt. Gladys takes a shuttle to go to the Messiah. When the five arrive, Shinn, Kira, and Cagalli enter the falling Messiah. Lunamaria and Athrun stay behind (in their Gundams) just in case, and the rest enter (Rey and Gladys enter in separate entrances).

Shinn confronts Durandal and they express their disappointment at each other; Durandal tells them that if they don't implement the Destiny Plan, the world will be tossed back into chaos thus starting the cycle of peace and war all over again. Shinn tells [Durandal] that he would rather move forward towards an uncertain future than be stuck in a peaceful present, and will fight if necessary. Durandal prepares to shoot but is shot by Rey instead. He tells Durandal that he accepts Shinn's future, a future full of hope. Talia orders the three [Shinn, Kira, Cagalli] to leave but before they do, she tells them that if possible, she would like for them to meet her son. Before they escape, Shinn decides to leave the Destiny behind; he also leaves the medal that saved his life in the cockpit. He boards the Force Impulse with Lunamaria and they all go out and head back to the Eternal.

Talia comforts Durandal in his final moments. She calls for Rey to come. Talia hugs her and comforts him too. The Messiah crashes and kills the three.

Lacus broadcasted a message across the battlefield, calling for everybody to stop fighting for more fighting would be meaningless. They all agree to a ceasefire.

C.E. 74; 10 months after the Battle of The Messiah, the peace talks are successful between Orb and ZAFT, finally ending the war. Shinn, Lunamaria, Cagalli, Athrun, Kira, and Lacus visit (they all met by chance) the cenotaph in Onogoro. Shinn says that he always hated the place but came to realize that no matter how bad the past, it should never decide your future. They all accept his apology and forgive him. They promise to fight together in the future. After paying their respects, they all went their separate ways.

Mu and Murrue, now retired, are living together in Orb. Andrew Waltfeld has opened his own coffee shop. Meyrin is working for ZAFT again and is training to be a Vice Captain. Dearka is promoted to a Red Coat. Miriallia is back as a freelance photographer. Erica Simmons is working on a next generation Gundam. Athrun serves as Cagalli's top military advisor.

Back in the PLANT Lacus became the Chairwoman and Kira is a White Coat Commander for ZAFT. Shinn is still a Red Coat. Athrun is an Orb admiral. Kira and Lacus run towards each other and hug in front of everybody surprising most of them.

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A/N #2: As to why Shinn left the Destiny in the Messiah. When Athrun told Shinn that " _Anyone who's ever wept cause they have felt weak, and powerless has had those kinds of thoughts, yes. But the moment you acquire all that power you've dreamt of you become the one who causes others to weep tears of lose._ " The Destiny was a symbol of the power Shinn dreamt of, but it was also the power that made others cry, so when the war ended, he didn't need that kind of power anymore and thus he let it go down with the Messiah.

A/N #3: And that's it. Sorry if it was confusing or rushed or both. Thank you for your time and patience.


End file.
